In Supreme Commander it worked pretty well though... I would be a fan of an autobuild feature yet I don't see it happen in Rebellion.
There are two main reasons that this works in Supreme Commander
The resource system in Supreme Commander was vastly different than Sins, being an "income vs. expenditures" system. As long as you were producing positives in both mass and power, you could build all night and day. Second, combat was much faster paced, many units being taken out in one or two hits (or multiple units in a single sweep if up against an experimental). So the demand to have such a scale of production was critical.
Harmful, you can put that start or stop whenever you want, just configure the fleet 1 as you would like, the 2 as you would like, and then only get started, and all factories will build your fleet, so we eliminate having to make a ship by ship in large fleets or set every time you got back a lost fleet.
I dont know about you, but if I lost my entire fleet I'd want to experiment with a new fleet anyway! 